[gmx-users] Re: Re[11]: Flat energy profile in g_wham

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Aug 31 21:56:03 CEST 2010


If you do decide to continue along with the method that I suggested,  
I'll join back in. To this point, I see no indication that you have  
tried to relate the force to the position for the water runs, which is  
my standing suggestion to you.


Quoting alexander yakovenko <yakovenko_a at ukr.net>:

> sure. Just note that I was only interested either profile is flat   
> and if g_wham identical for pullf and pullx, so 4 windows about 36   
> ps, 1 ps output.
> Alex
>   Can you post a snip of your pullx and pullf files from the water box
> simulation where you pulled on 2 waters?
> Quoting alexander yakovenko <yakovenko_a at ukr.net>:
>> Yep, my case is b  :(... Gromacs do writes pullx as ref COM global
>> coords and pull COM displacement. And I still don't realize what is
>> force value in pullf but it gives identical results for both -if and
>> -ix options of g_wham. And g_wham do works OK at least for 2 waters
>> separation in 0.3-1nm scale... probably my run should produce snaps
>> more frequently, say each ps... will try this.
>> Regards,
>> Alex
>> Sorry Alex, but there is no good substitute what I have already
>> suggested. I helped you find a lead and I suggested a way to simplify
>> your system to discover what is going on. Now it's up to you to do
>> that work.
>> It might end up being a bug, but I doubt it. I have done things
>> similar to what you are doing and have no problems. And even if it is
>> a bug, then the developers will need you to find a simple version of
>> the problem in any event.
>> Make the water box, pull two waters, try to match up the force and
>> energy values from your pull output files.
>> Note that you have forgotten the 1/2 factor in your energy function so
>> there is no factor of 2 in your force. Also, the force is the negative
>> derivative. Check the manual for the exact equations.
>> Chris.
>> Quoting alexander yakovenko <yakovenko_a at ukr.net>:
>>> It is 2 options why I can?t understand relation between pullf and
>>> pullx: either I have no imagine how they should related or they
>>> related so that one can?t even imagine (say due to bug or file
>>> format). Till now my view was that we need a force to keep two
>>> molecules at asked separation. The force is F=2*k*x (or 2*k*|r| in
>>> case of Y Y Y) and work spent on this is k*x^2. Thus in pullx we
>>> have either a) coordinates of COMs of both groups or b) COM of
>>> reference group and relative displacement of pulling group and in
>>> pullf we have 2*k*x values. The problem is that I can?t substitute
>>> data from pullx so to get data from pullf and thus I don?t realize
>>> these relations. Say pullx line is 11984.0000
>>> 3.12086 4.37951 -1.63297 1.98567 2.64212
>>> -3.25943 so |r| is a) 4.641936 if dx, dy and dz are displacements
>>> or b) 2.63676933 if dx, dy and dz are just coordinates of
>>> pulling group COM. Suggesting |ro| to be 2.383+1.0=3.383 nm
>>> (equilibrated complex position + displacement of 1.0 nm) and k=1000
>>> kJ/mol/nm^2 we have force of a) 9283.871 or b)
>>> 5273.53865 kJ/mol/nm. Unfortunately neither of these values
>>> looks like 332.586 from pullf file... So can you please help
>>> me to choose my option: a) mdrun is corrupted, b) I don?t
>>> understand what I am doing or c) pullf and pullx writes some
>>> specific format of output that should be processed by g_wham to
>>> make some sense? Because if it is a) I have to post bugzilla, if b)
>>> I have to deal with water, if c) I have to post gromacs-users in
>>> order to launch g_wham.
>>> Regards,
>>> Alex
>>> >
>>> >
>>> So now we have the first real lead. Next is for you to simplify your
>>> system to the point where you *can* understand the relationship
>>> between the pullf and pullx files. For example, I always suggest a
>>> water bath of explicit water with the sd integrator and apply the pull
>>> code to two waters.
>>> It's time for you to bash your head against this one on your own until
>>> you can find a simple system that has no problem and then a slightly
>>> more complex system that has the problem. Bring those back to the list
>>> and we can help again if you can;t figure it out.
>>> PS: you should file a bugzilla or otherwise try to get the gromacs
>>> list fixed so that you can post directly.
>>> Chris.
>>> Quoting alexander yakovenko < yakovenko_a at ukr.net >:
>>> > Sorry for mixing things, I do pull into N Y N direction and then
>>> > performed umbrella simulation at Y Y Y for each distances window.
>>> > This is very good question, actually I don't realize it too. The only
>>> > thing what I can say is that I haven't edited/renamed these files,
>>> > just copy them. So this is pure output of mdrun, hopes it knows what
>>> > it writes... I can provide a tpr of a window for example so you can
>>> > check couple first strings (for reproduction, I carried out all
>>> > calculations on 8x Xeons at 2.66 workstations).
>>> > Alex
>>> > >
> Alexander Yakovenko
> Institute of Molecular Biology & Genetic of NAS of Ukraine
> 03143
> acad.Zabolotnogo str. 150
> Kiev
> Ukraine
> ______________________________________________
> E-mail: yakovenko_a at ukr.net

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